Crews will start work on an Amtrak train layover facility in Brunswick next month even though the Board of Environmental Protection could kill the project if it rules in favor of a neighborhood group that is appealing a decision to allow construction.

Clearing of the site will start as early as Sept. 14 and the superstructure is scheduled to be built this fall, said Matt Tonello, project executive with Consigli Construction, which is building the $12.4 million, 60,000-square-foot train shed. Company officials will meet Friday with state Department of Environmental Protection staffers for a final review of plans to handle stormwater runoff and contaminated soils on the site during construction. The site is an abandoned rail yard polluted with coal ash.

The Northern New England Passenger Rail Authority, which manages the Downeaster train service, has all the necessary permits to begin construction and is confident that the appeal will be rejected, said Patricia Quinn, the authority’s director.

“We’ve got a good plan,” she said. “The Department of Environmental Protection says we have met the standards. We are moving forward.”

The Brunswick West Neighborhood Coalition is appealing DEP Commissioner Patricia Aho’s June 16 decision to give the rail authority a stormwater permit. In its 18-page appeal to the Board of Environmental Protection, the group says that the rail authority’s plan for managing stormwater is unreliable and that the project will disturb the polluted site and threaten the health of nearby residents.

The group argues that Aho approved the permit with an “unprecedented” list of special conditions that sought to bring the project in compliance with state law. By approving an incomplete application and then trying to fix its deficiencies, the group argues, Aho denied the public an opportunity to provide comment on the special conditions.

The group, which filed its appeal July 16, last month asked Aho to stay her decision to award the permit pending a decision on the appeal. Aho rejected that request.

In an Aug. 11 letter, Aho said the rail authority’s application met the requirements of state law and that many of the conditions added by the DEP go “above and beyond” the law and were imposed to address concerns raised by residents.

Residents have opposed the facility because of noise and pollution concerns.

Tonello said work crews will be capping the site and reducing the risk of groundwater pollution.

“They will end up with a much cleaner site, obviously with a building on it, than what they’re seeing today,” he said.

The building’s design incorporates concrete blocks encased in a layer of sound-proofing foam insulation to mitigate noise from trains inside the shed. Tonello said the construction schedule calls for the building’s superstructure to be erected before winter and for the project to be completed by early July.

Quinn said it’s important to begin construction on the project, which was first proposed four years ago, to contain costs and to improve the Brunswick service before the start of next year’s summer tourism season. The rail authority plans to add a third, daily round-trip train between Boston and Brunswick next summer. It can only add the service if the trains can stay overnight in the new Brunswick facility, she said.

The Board of Environmental Protection, which is made up of seven citizens appointed by the governor and confirmed by the Legislature, has broad power to review the decisions of state regulators. It can affirm, amend or reverse Aho’s decision, or it can remand the matter to her for further consideration.

In 2013, the board overturned Aho’s decision to reject a permit for a wind power project on Passadumkeag Mountain. The board granted the permit. Maine’s Supreme Judicial Court later upheld the BEP decision after a local group appealed it.

The appeal process is a long one. It took four months for the board to rule on the Passadumkeag appeal and a year for the issue to be resolved through the courts.

The board, whose current members all have been appointed by Gov. Paul LePage, has yet to set a date to hear oral arguments for the Brunswick appeal.

Residents from the Brunswick West Neighborhood Coalition could not be reached for comment Thursday night.

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